7SH1 | pdb_00007sh1

Class II UvrA protein - Ecm16

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VF7
experimental model	PDB	2VF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	0.1 M MES pH 6.5, 0.2 M sodium thiocyanate, 12 % PEG (w/v) 20K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.13	α = 90
b = 141.13	β = 90
c = 173.614	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 9M		2017-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.04	173.614	100	0.086	0.089	0.02	0.999	23.5	20.4		127062			38.4565860718

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.041	2.076			1.472	0.475	0.796	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2VF8	2.04	122.22	120796	6154	100	0.19969	0.19764	0.2	0.23903	0.24	RANDOM	46.778

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.02	0.01		0.02		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.439
r_dihedral_angle_4_deg	15.758
r_dihedral_angle_3_deg	14.52
r_long_range_B_refined	8.583
r_long_range_B_other	8.579
r_scangle_other	6.877
r_dihedral_angle_1_deg	6.496
r_mcangle_it	5.688
r_mcangle_other	5.688
r_scbond_it	4.877
r_scbond_other	4.877
r_mcbond_it	4.371
r_mcbond_other	4.37
r_angle_refined_deg	1.99
r_angle_other_deg	1.108
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9265
Nucleic Acid Atoms
Solvent Atoms	612
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing